Table 1.

Data sets used for testing and comparison of NGSEP with other algorithms for SNV and CNV detection and genotyping

Data set (coverage)	NGSEP		CNVNator		BreakDancer		GATKb		SNVer		SAMtools		VarScan 2
	RTa	RAMa	RT	RAM	RT	RAM	RT	RAM	RT	RAM	RT	RAM	RT	RAM
Yeast parent CBS6412 (79×)	27 min	1.9 Gb	1 min	1.6 Gb	1 min	10 Mb	1 h 41 min	4.0 Gb	11 min	2.6 Gb	14 min	40 Mb	38 min	5.8 Gb
Yeast parent ER7A (96×)	30 min	2 Gb	1 min	1.6 Gb	1 min	10 Mb	1 h 58 min	4.1 Gb	14 min	2.7 Gb	17 min	40 Mb	36 min	5.8 Gb
Yeast pool (34×)	21 min	1.6 Gb	1 min	1.6 Gb	1 min	15 Mb	1 h 35 min	3.4 Gb	7 min	2.7 Gb	6 min	35 Mb	26 min	5.8 Gb
Rice IR8 (26×)	2 h 38 min	3 Gb	25 min	2.3 Gb	2 h 23 min	2.8 Gb	11 h 21 min	5.8 Gb	–	–	2 h 43 min	100 Mb	–	–
Human chr1 (64×)	1 h 44 min	2.7 Gb	19 min	2.1 Gb	15 min	400 Mb	1 h 37 min	200 Mb	1 h 51 min	2.8 Gb	1 h 28 min	300 Mb	–	–
Human (5×)	9 h 25 min	7.5 Gb	3 h 46 min	7.4 Gb	24 min	500 Mb	8 h 20 min	600 Mb	–	–	5 h 23 min	300 Mb	–	–

^a RT: runtime; RAM: random access memory.

^b The GATK pipeline was executed as suggested in (9) for the yeast and rice samples. For the human samples only the Unified Genotyper was executed.